1 | # Note: model title and parameter table are inserted automatically |
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2 | r""" |
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3 | This model provides the scattering intensity, *I(q)*, for a lyotropic lamellar phase where a random distribution in |
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4 | solution are assumed. The SLD of the head region is taken to be different from the SLD of the tail region. |
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5 | |
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6 | *2.1.31.1. Definition* |
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7 | |
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8 | The scattering intensity *I(q)* is |
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9 | |
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10 | .. math:: |
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11 | |
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12 | I(Q) = 2\pi{P(Q) \over (2(|delta|\ H +|delta|\ T) Q^2) |
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13 | |
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14 | The form factor is |
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15 | |
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16 | .. image:: img/lamellarFFHG_.jpg |
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17 | |
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18 | where |delta|\ T = tail length (or *tail_length*), |delta|\ H = head thickness (or *h_thickness*), |
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19 | |drho|\ H = SLD(headgroup) - SLD(solvent), and |drho|\ T = SLD(tail) - SLD(solvent). |
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20 | |
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21 | The 2D scattering intensity is calculated in the same way as 1D, where the *q* vector is defined as |
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22 | |
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23 | .. math:: |
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24 | |
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25 | Q = \sqrt{Q_x^2 + Q_y^2} |
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26 | |
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27 | The returned value is in units of |cm^-1|, on absolute scale. In the parameters, *sld_tail* = SLD of the tail group, |
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28 | and *sld_head* = SLD of the head group. |
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29 | |
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30 | ============== ======== ============= |
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31 | Parameter name Units Default value |
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32 | ============== ======== ============= |
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33 | background |cm^-1| 0.0 |
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34 | head_sld |Ang^-2| 3e-06 |
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35 | scale None 1 |
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36 | solvent_sld |Ang^-2| 6e-06 |
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37 | head_length |Ang| 10 |
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38 | tail_length |Ang| 15 |
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39 | sld (tail) |Ang^-2| 0 |
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40 | ============== ======== ============= |
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41 | |
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42 | .. image:: img/lamellarFFHG_138.jpg |
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43 | |
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44 | *Figure. 1D plot using the default values (w/1000 data point).* |
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45 | |
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46 | Our model uses the form factor calculations implemented in a c-library provided by the NIST Center for Neutron Research |
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47 | (Kline, 2006). |
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48 | |
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49 | REFERENCE |
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50 | |
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51 | F Nallet, R Laversanne, and D Roux, J. Phys. II France, 3, (1993) 487-502 |
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52 | |
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53 | also in J. Phys. Chem. B, 105, (2001) 11081-11088 |
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54 | |
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55 | *2014/04/17 - Description reviewed by S King and P Butler.* |
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56 | """ |
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57 | |
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58 | from numpy import pi, inf |
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59 | |
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60 | name = "lamellar_FFHG" |
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61 | title = "Random lamellar phase with Head Groups " |
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62 | description = """\ |
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63 | [Random lamellar phase with Head Groups] |
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64 | I(q)= 2*pi*P(q)/(2(H+T)*q^(2)), where |
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65 | P(q)= see manual |
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66 | layer thickness =(H+T+T+H) = 2(Head+Tail) |
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67 | sld = Tail scattering length density |
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68 | sld_head = Head scattering length density |
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69 | sld_solvent = solvent scattering length density |
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70 | background = incoherent background |
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71 | scale = scale factor |
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72 | """ |
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73 | |
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74 | parameters = [ |
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75 | # [ "name", "units", default, [lower, upper], "type", |
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76 | # "description" ], |
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77 | [ "tail_length", "Ang", 15, [0, inf], "volume", |
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78 | "Tail thickness" ], |
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79 | [ "head_length", "Ang", 10, [0, inf], "volume", |
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80 | "head thickness" ], |
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81 | [ "sld", "1e-6/Ang^2", 0.4, [-inf,inf], "", |
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82 | "Tail scattering length density" ], |
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83 | [ "head_sld", "1e-6/Ang^2", 3.0, [-inf,inf], "", |
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84 | "Head scattering length density" ], |
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85 | [ "solvent_sld", "1e-6/Ang^2", 6, [-inf,inf], "", |
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86 | "Solvent scattering length density" ], |
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87 | ] |
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88 | |
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89 | # No volume normalization despite having a volume parameter |
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90 | # This should perhaps be volume normalized? |
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91 | form_volume = """ |
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92 | return 1.0; |
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93 | """ |
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94 | |
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95 | Iq = """ |
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96 | const double qsq = q*q; |
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97 | const double drh = head_sld - solvent_sld; |
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98 | const double drt = sld - solvent_sld; //correction 13FEB06 by L.Porcar |
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99 | const double qT = q*tail_length; |
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100 | double Pq, inten; |
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101 | Pq = drh*(sin(q*(head_length+tail_length))-sin(qT)) + drt*sin(qT); |
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102 | Pq *= Pq; |
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103 | Pq *= 4.0/(qsq); |
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104 | |
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105 | inten = 2.0e-4*M_PI*Pq/qsq; |
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106 | |
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107 | return inten /= 2.0*(head_length+tail_length); //normalize by the bilayer thickness |
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108 | |
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109 | """ |
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110 | |
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111 | Iqxy = """ |
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112 | // never called since no orientation or magnetic parameters. |
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113 | return -1.0; |
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114 | """ |
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115 | |
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116 | # ER defaults to 0.0 |
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117 | # VR defaults to 1.0 |
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118 | |
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119 | demo = dict( |
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120 | scale=1, background=0, |
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121 | tail_length=15,head_length=10, |
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122 | sld=0.4, head_sld=3.0, solvent_sld=6.0, |
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123 | tail_length_pd= 0.2, tail_length_pd_n=40, |
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124 | head_length_pd= 0.01, head_length_pd_n=40, |
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125 | ) |
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126 | oldname = 'LamellarFFHGModel' |
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127 | oldpars = dict(head_length='h_thickness', sld='sld_tail', head_sld='sld_head', solvent_sld='sld_solvent') |
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128 | |
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